ATAC-seq on motrpac
Report generated at 2018-10-27 03:55:57
Pipeline type: ATAC-Seq
Peak caller: MACS2
| rep1 | rep2 | |
|---|---|---|
| Total | 43339412 | 65787412 |
| Total(QC-failed) | 0 | 0 |
| Dupes | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 |
| Mapped | 43062943 | 64369053 |
| Mapped(QC-failed) | 0 | 0 |
| % Mapped | 99.3600 | 97.8400 |
| Paired | 24584078 | 32781498 |
| Paired(QC-failed) | 0 | 0 |
| Read1 | 12292039 | 16390749 |
| Read1(QC-failed) | 0 | 0 |
| Read2 | 12292039 | 16390749 |
| Read2(QC-failed) | 0 | 0 |
| Properly Paired | 24066130 | 31075436 |
| Properly Paired(QC-failed) | 0 | 0 |
| % Properly Paired | 97.8900 | 94.8000 |
| With itself | 24260918 | 31308026 |
| With itself(QC-failed) | 0 | 0 |
| Singletons | 46691 | 55113 |
| Singletons(QC-failed) | 0 | 0 |
| % Singleton | 0.1900 | 0.1700 |
| Diff. Chroms | 52333 | 59446 |
| Diff. Chroms (QC-failed) | 0 | 0 |
| rep1 | rep2 | |
|---|---|---|
| Total | 16972830 | 18904942 |
| Total(QC-failed) | 0 | 0 |
| Dupes | 0 | 0 |
| Dupes(QC-failed) | 0 | 0 |
| Mapped | 16972830 | 18904942 |
| Mapped(QC-failed) | 0 | 0 |
| % Mapped | 100.0000 | 100.0000 |
| Paired | 16972830 | 18904942 |
| Paired(QC-failed) | 0 | 0 |
| Read1 | 8486415 | 9452471 |
| Read1(QC-failed) | 0 | 0 |
| Read2 | 8486415 | 9452471 |
| Read2(QC-failed) | 0 | 0 |
| Properly Paired | 16972830 | 18904942 |
| Properly Paired(QC-failed) | 0 | 0 |
| % Properly Paired | 100.0000 | 100.0000 |
| With itself | 16972830 | 18904942 |
| With itself(QC-failed) | 0 | 0 |
| Singletons | 0 | 0 |
| Singletons(QC-failed) | 0 | 0 |
| % Singleton | 0.0000 | 0.0000 |
| Diff. Chroms | 0 | 0 |
| Diff. Chroms (QC-failed) | 0 | 0 |
| rep1 | rep2 | |
|---|---|---|
| Unpaired Reads | 0 | 0 |
| Paired Reads | 9395807 | 10681883 |
| Unmapped Reads | 0 | 0 |
| Unpaired Dupes | 0 | 0 |
| Paired Dupes | 909392 | 1229412 |
| Paired Opt. Dupes | 4567 | 4432 |
| % Dupes/100 | 0.0968 | 0.1151 |
| rep1 | rep2 | |
|---|---|---|
| Total Read Pairs | 9171371 | 10562098 |
| Distinct Read Pairs | 8323666 | 9372160 |
| One Read Pair | 7544689 | 8295254 |
| Two Read Pairs | 715743 | 974306 |
| NRF = Distinct/Total | 0.9076 | 0.8873 |
| PBC1 = OnePair/Distinct | 0.9064 | 0.8851 |
| PBC2 = OnePair/TwoPair | 10.5411 | 8.5140 |
NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally
| rep1 | rep2 | |
|---|---|---|
| Reads | 8311019 | 9357705 |
| Est. Fragment Len. | 0 | 0 |
| Corr. Est. Fragment Len. | 0.1949 | 0.1503 |
| Phantom Peak | 70 | 60 |
| Corr. Phantom Peak | 0.1581 | 0.1295 |
| Argmin. Corr. | 1500 | 1500 |
| Min. Corr. | 0.1128 | 0.1218 |
| NSC | 1.7272 | 1.2340 |
| RSC | 1.8135 | 3.7017 |
NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.
| rep1 | rep2 | rep1-pr1 | rep2-pr1 | rep1-pr2 | rep2-pr2 | pooled | ppr1 | ppr2 | |
|---|---|---|---|---|---|---|---|---|---|
| Fraction of Reads in Peak | 0.2670 | 0.1432 | 0.2931 | 0.1753 | 0.2922 | 0.1742 | 0.1896 | 0.2034 | 0.2025 |
| overlap | IDR | |
|---|---|---|
| Nt | 87204 | 26262 |
| N1 | 93092 | 41952 |
| N2 | 38760 | 14980 |
| Np | 107775 | 47189 |
| N optimal | 107775 | 47189 |
| N conservative | 87204 | 26262 |
| Optimal Set | ppr | ppr |
| Conservative Set | rep1-rep2 | rep1-rep2 |
| Rescue Ratio | 1.2359 | 1.7969 |
| Self Consistency Ratio | 2.4018 | 2.8005 |
| reproducibility | borderline | borderline |
Overlapping peaks
IDR (Irreproducible Discovery Rate) peaks
| rep1-rep2 | rep1-pr | rep2-pr | ppr | |
|---|---|---|---|---|
| Fraction of Reads in Peak | 0.1147 | 0.1890 | 0.0445 | 0.1302 |
| rep1-rep2 | rep1-pr | rep2-pr | ppr | |
|---|---|---|---|---|
| Fraction of Reads in Peak | 0.0605 | 0.1277 | 0.0260 | 0.0855 |